Parul tew wrote:
Hello,
I get the following error when I try to run grompp cpmmand for energy
minimization in GROMACS of DPPC membrane
...
checking input for internal consistency...
processing topology...
---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 843
Fatal error:
Atomtype HW not found
Per the tutorial, step 2: "Non-bonded interactions involving atom type HW are
also present; since these are all zero you can delete these lines as well, or
otherwise rename HW as H to be consistent with the GROMOS96 53a6 naming convention."
the topology file of the DPPC contains:
--
; This is your topology file
; 1SOL OW1 -2.449 -4.190 -1.80
;
; Include chain topologies
#include "ffG53a6_lipid.itp"
#include "dppc.itp"
; Include water topology
;include "spc.itp"
; Include ion topologies
;include "ions.itp"
You're going to have problems here, as well. You've commented out the water and
ion topologies. The next fatal error is surely going to be "Moleculetype SOL
not defined" or the like.
-Justin
; System specifications
[ system ]
128-Lipid DPPC Bilayer
[ molecules ]
; molecule name nr.
DPPC 128
SOL 3655
I am using ffG53a6
thanks
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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